The disclosures herein relate generally to roughness measurements of pattern structures, and more particularly, to roughness measurements of pattern structures in noise-prone images, such as in images formed when using a scanning electron microscope (SEM) or other imaging apparatus that produce images including undesired noise, and even more particularly, to calibrating a machine-learning based model such as a lithography/etch/patterning model or a metrology model using the roughness measurements of pattern structures.